MolNFT v1 · #179989 · protein
Structure of spop math domain in complex with a geminin peptide
7KLZ · Speckle-type poz protein: “Structure of spop math domain in complex with a geminin peptide”. X-ray diffraction, 1 ligand (PO4), 3 pockets (best druggability 0.45). MolNFT v1 #179989 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7KLZ
- Type
- protein
- Length
- 295 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Speckle-type poz protein; Geminin peptide
- UniProt
- O43791, O75496
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Speckle-type poz protein | protein | 138 | 11% helix, 48% strand | O43791 |
| B | Speckle-type poz protein | protein | 139 | 10% helix, 48% strand | O43791 |
| C, D | Geminin peptide | protein | 9 | 0% helix, 11% strand | O75496 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.45 | 0.76 | 24 | empty |
| 2 | 105 | 0.43 | 0.78 | 19 | empty |
| 3 | 83 | 0.40 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 634 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 478 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 426 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7KLZ · Structure of SPOP MATH domain in complex with a Geminin peptide · the same entry in another collection · chain D against D, TM-score 1.00
- O43791 · AlphaFold monomer V2.0 prediction for speckle-type poz protein (O43791) · a predicted model of the same protein · chain A against A, TM-score 0.93
- O75496 · AlphaFold monomer V2.0 prediction for geminin (O75496) · a predicted model of the same protein · chain D against A, TM-score 0.26
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O43791
- Every structure of UniProt O75496
- Elsewhere: RCSB PDB 7KLZ · PDBe 7KLZ · UniProt O43791 · UniProt O75496
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